Equipment in the Facility
The facility has the following equipment: 10XGenomics Chromium system, BD Rhapsody, Bio-Rad ddSeq, MissionBio Tapestri, Fluidigm C1, Fluidigm Biomark, SPT Mosquito, Formulatrix Mantis, Beckman FxP, Agilent Bioanalyzer, Agilent Fragment Analyzer, Agilent Tapestation
10XGenomics Chromium System
Our most popular system enables upto 80000 single cells to be partitioned into microfluidic droplets with a barcoded bead. Kits are available for single cell 3' & 5' RNASeq, targeted gene panels, ATAC-Seq, TCR/BCR, and combined RNA/ATAC . Also can be used for simultaneous proteomic targets using barcoded antibodies available from BioLegend, BD, or made in house using our custom antibody labeling service.
BD Rhapsody Express
A lower cost alternative to the Chromium, this system enables 10000s of cells to be captured in microfluidic wells via gravity. Kits for single cell whole exome RNASeq, targeted gene expression and TCR/BCR are available and the kits can be used in conjunction with single cell proteomics using BD Abseq/BioLegend Totalseq or our in house antibody labeling service. The system is generally the cheapest option for single cell RNASeq when superloaded, and is gentler to cells than the Chromium. A large volume of cells can be inserted into this system, avoiding cell pelleting steps. Further information.
Bio-Rad ddSeq
This system offers single cell ATAC-Seq at a lower cost and greater efficiency than other systems. Many 1000s of cells can be loaded and capture efficiency is 80-90%. This system can also be used for low cost Drop-seq methods. Further information.
MissionBio Tapestri
This system allows simultaneous detection of DNA SNVs, CNVs, and protein in thousands of single-cells. More information.
Fluidigm Biomark QPCR system
The Biomark can run microfluidic chips for massively parallel QPCR of 1-100 cell samples or cDNA from larger samples. The system utilises low volumes of standard gene expression or genotyping Taqman probes for analysis and so is very flexible and can be very cost and time effective.
Different chip formats are available: 24 genes in 192 samples, 48 genes in 48 samples, or 96 genes in 96 samples. A flexible chip modular and reusable chip is also available for upto 72 samples. Further information.
Robotics Liquid Handlers - Beckman FxP/4000, SPT Mosquito & Formulatrix mantis
These robots can automate most genomic assays to provide consistency and scalability and are particularly useful for large scale projects. Automated protocols currently available: Ampure Magnetic bead clean ups (96/384 plates), QPCR (96/384 plates), sample pooling and normalisation (multiple 96/384 plates), SmartSeq RNAseq, plate reformatting (96 to 384 etc), Illumina Nextera library preparation. The Mosquito and Mantis robots allow miniaturisation of assays to save on reagent cost. Assays that have been successfully miniaturised so far: QPCR, Illumina library prep, PicoGreen, Kapa Illumina library quantification, whole genome amplification.
Agilent Bioanalyzer, Tapestation 4200, Fragment Analyzer
These systems can be used to analyse tiny amounts of protein, RNA or DNA conveniently. The Fragment Analyser can analyse up to 192 samples at a time and has a 2bp DNA resolution enabling convenient genotyping.
Commonly analyzed nucleic acid samples include:
- Genomic DNA
- Large Fragment DNA
- Small Fragment DNA
- Cell-free DNA (cfDNA)
- NGS Libraries (Illumina and PacBio)
- Plasmid (supercoild and linear)
- SSR/Microsatellites
- PCR Amplicons
- Restriction Enzyme Digests
- Small RNA NGS Libraries
- mRNA
- sgRNA
- Small RNA/microRNA
- Ribo-Depleted Total RNA
- Total RNA
- FFPE extracted nucleic acids